Electronic and vibrational circular dichroism spectroscopic study of non-covalent interactions of meso-5,10,15,20-tetrakis(1-methylpyridinium-4-yl)porphyrin with (dG-dC)10 and (dA-dT)10

Nový, Jakub; Urbanová, Marie; Volka, K.

doi:10.1016/j.vibspec.2006.06.020

Cited by 10 publications

(5 citation statements)

References 23 publications

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“…This change of the spectral pattern may indicate that the conformational change from right-handed to left-handed occurred. 35 The UV-ECD spectrum also change its shape substantially, and had a negative couplet, with a maximum at 262(þ), and two minima at 270(À) and 247(À) nm, typical of the B to Z form transition. 11,34 The UV-ECD results correlate with the results on induced CD in the Soret region: both signals reverse the sign of their pattern.…”

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Vibrational and electronic circular dichroism study of the interactions of cationic porphyrins with (dG‐dC)₁₀and (dA‐dT)₁₀

Nový

Urbanová

2006

Biopolymers

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The interactions of two different porphyrins, without axial ligands-5,10,15,20-tetrakis(1-methylpyridinium-4-yl)porphyrin-Cu(II) tetrachloride (Cu(II)TMPyP) and with bulky meso substituents-5,10,15,20-tetrakis(N,N,N-trimethylanilinium-4-yl)porphyrin tetrachloride (TMAP), with (dG-dC)10 and (dA-dT)10 were studied by combination of vibrational circular dichroism (VCD) and electronic circular dichroism (ECD) spectroscopy at different [oligonucleotide]/[porphyrin] ratios, where [oligonucleotide] and [porphyrin] are the concentrations of oligonucleotide per base-pair and porphyrin, respectively. The combination of VCD and ECD spectroscopy enables us to identify the types of interactions, and to specify the sites of interactions: The intercalative binding mode of Cu(II)TMPyP with (dG-dC)(10), which has been well described, was characterized by a new VCD "marker" and it was shown that the interaction of Cu(II)TMPyP with (dA-dT)10 via external binding to the phosphate backbone and major groove binding caused transition from the B to the non-B conformer. TMAP interacted with the major groove of (dG-dC)10, was semi-intercalated into (dA-dT)10, and caused significant variation in the structure of both oligonucleotides at the higher concentration of porphyrin. The spectroscopic techniques used in this study revealed that porphyrin binding with AT sequences caused substantial variation of the DNA structure. It was shown that VCD spectroscopy is an effective tool for the conformational studies of nucleic acid-porphyrin complexes in solution.

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“…On the basis of these spectral changes, we suggest that major groove binding took place. 35 At the molar ratio of 4/1, the positive VCD couplet at 1699(À)/1684(þ) cm…”

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Vibrational and electronic circular dichroism study of the interactions of cationic porphyrins with (dG‐dC)₁₀and (dA‐dT)₁₀

Nový

Urbanová

2006

Biopolymers

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“…The VCD spectra of d(GGGA) 5 are clearly different from the VCD spectra of calf thymus DNA, (dG-dC) 10 and (dA-dT) 10 studied by us before. [34][35][36] Because of the intrinsic sensitivity of VCD to the spatial arrangement, the observations reflect different structures of these systems. The samples of d(GGGA) 5 in presence of Li 1 , Na 1 , and K 1 ions were characterized by the nondenaturing electrophoresis (see Figure 3).…”

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Formation and temperature stability of G‐quadruplex structures studied by electronic and vibrational circular dichroism spectroscopy combined with ab initio calculations

et al. 2007

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Variations in the structure of d(GGGA)(5) oligonucleotide in the presence of Li(+), Na(+), and K(+) ions and its temperature stability were studied using electronic and vibrational circular dichroism, IR absorption, and ab initio calculations with the Becke 3-Lee-Yang-Parr functional at the 6-31G** level. The samples were characterized by nondenaturing gel electrophoresis. Oligonucleotide d(GGGA)(5) in the presence of Li(+) forms a nonplanar single tetramer, with angles of 102 degrees and 171 degrees between neighboring guanine bases. This tetramer changes its geometry at temperatures >50 degrees C, but does not form a quadruplex structure. In the presence of Na(+), the d(GGGA)(5) structure was optimized to almost planar tetramers with an angle of 177 degrees between neighboring guanines. The spectral results suggest that it stacks into a quadruplex helical structure. This quadruplex structure decayed to a single tetramer at temperatures >60 degrees C. The Hartree-Fock energies imply that d(GGGA)(5) prefers to form complexes with Na(+) rather than Li(+). The d(GGGA)(5) structure in the presence of monovalent ions is stabilized against thermal denaturation in the order Li(+) < Na(+) < K(+).

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“…Hence, a change from monomeric binding to outside stacking reduces both the spectral shift and hypochromicity. 28,29 Comparing the absorption change of H 2 TMPyP and B-TMPyP upon binding to CTDNA, their spectral shifts as well as the hypochromicity was very similar. This similarity may suggest that the magnitude of interaction or the interaction type of BTMPyP with CTDNA was comparable to the case of intercalated H 2 TMPyP.…”

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Direct Stacking of Non-metallic Planar Porphyrin to DNA

2008

Bulletin of the Korean Chemical Society

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Porphyrins generally bind DNA in two different ways with respect to the mixing ratio; monomeric binding at a low mixing ratio and outside stacking at a high mixing ratio. In the present study, CTDNA binding property of a planar structured porphyrin, 5,10,15,20-tetrakis(N-methyl-4-pyridin-4-yl-phenyl)porphyrin (referred to as B-TMPyP) was investigated using absorption, CD, LD, and LD r spectroscopies. B-TMPyP produced a bisignate CD band, even at the lowest mixing ratio, indicating that B-TMPyP may not have a monomeric binding mode. From the observations of the spectral changes to the absorption, CD, and LD spectra in mixing ratio dependent titrations, B-TMPyP seems to have a quite different stacking type compared to that for the binding of H2TMPyP. Moreover, B-TMPyP produced a CD band of opposite shape in the Soret band region. A qualitative explanation for the observed optical differences is also given.

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Electronic and vibrational circular dichroism spectroscopic study of non-covalent interactions of meso-5,10,15,20-tetrakis(1-methylpyridinium-4-yl)porphyrin with (dG-dC)10 and (dA-dT)10

Cited by 10 publications

References 23 publications

Vibrational and electronic circular dichroism study of the interactions of cationic porphyrins with (dG‐dC)₁₀and (dA‐dT)₁₀

Vibrational and electronic circular dichroism study of the interactions of cationic porphyrins with (dG‐dC)₁₀and (dA‐dT)₁₀

Formation and temperature stability of G‐quadruplex structures studied by electronic and vibrational circular dichroism spectroscopy combined with ab initio calculations

Direct Stacking of Non-metallic Planar Porphyrin to DNA

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Electronic and vibrational circular dichroism spectroscopic study of non-covalent interactions of meso-5,10,15,20-tetrakis(1-methylpyridinium-4-yl)porphyrin with (dG-dC)10 and (dA-dT)10

Cited by 10 publications

References 23 publications

Vibrational and electronic circular dichroism study of the interactions of cationic porphyrins with (dG‐dC)10and (dA‐dT)10

Vibrational and electronic circular dichroism study of the interactions of cationic porphyrins with (dG‐dC)10and (dA‐dT)10

Formation and temperature stability of G‐quadruplex structures studied by electronic and vibrational circular dichroism spectroscopy combined with ab initio calculations

Direct Stacking of Non-metallic Planar Porphyrin to DNA

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Vibrational and electronic circular dichroism study of the interactions of cationic porphyrins with (dG‐dC)₁₀and (dA‐dT)₁₀

Vibrational and electronic circular dichroism study of the interactions of cationic porphyrins with (dG‐dC)₁₀and (dA‐dT)₁₀